function b = setEmissionProbabilities
% setEmissionProbabilities this function sets the emission
% probabilities for the 7 states as specified in the code

N = 4;

b = zeros(N,84);

% state 1
b(1,1:4) = 0.25;

% state 2 (direct start codon) : P(ATG) = 0.905, P(GTG) = 0.090, P(TTG)=0.005
b(2, 1*(4^2) + 4*(4) + 3) = 0.905;
b(2, 3*(4^2) + 4*(4) + 3) = 0.090;
b(2, 4*(4^2) + 4*(4) + 3) = 0.005;

% state 3 (direct coding region)
b(3, 1:4) = 0.25;

% state 4 (direct stop codon) : P(TAG) = 0.4, P(TAA) = 0.4, P(TGA) = 0.2
b(4, 4*(4^2) + 1*(4) + 3) = 0.4;
b(4, 4*(4^2) + 1*(4) + 1) = 0.4;
b(4, 4*(4^2) + 3*(4) + 1) = 0.2;

% % state 5(reverse stop codon) : P(CTA) = 0.4, P(TTA) = 0.4, P(TCA) = 0.2
% b(5, 2*(4^2) + 4*(4^1) + 1) = 0.4;
% b(5, 4*(4^2) + 4*(4^1) + 1) = 0.4;
% b(5, 4*(4^2) + 2*(4^1) + 1) = 0.2;
% 
% % state 6 (reverse coding region)
% b(6, 1:4) = 0.25;
% 
% % state 7 (reverse start codon):P(CAT) = 0.905, P(CAC) = 0.09, P(CAA) =
% % 0.005
% b(7, 2*(4^2) + 1*4 + 4) = 0.905;
% b(7, 2*(4^2) + 1*4 + 2) = 0.090;
% b(7, 2*(4^2) + 1*4 + 1) = 0.005;

end
